The Swr1 chromatin-remodeling complex prevents genome instability induced by replication fork progression defects

Anjana Srivatsan,Bin-Zhong Li,Dana Branzei,Christopher D Putnam,Richard D Kolodner,Barnabas Szakal

doi:10.1038/s41467-018-06131-2

Abstract

Genome instability is associated with tumorigenesis. Here, we identify a role for the histone Htz1, which is deposited by the Swr1 chromatin-remodeling complex (SWR-C), in preventing genome instability in the absence of the replication fork/replication checkpoint proteins Mrc1, Csm3, or Tof1. When combined with deletion of SWR1 or HTZ1, deletion of MRC1, CSM3, or TOF1 or a replication-defective mrc1 mutation causes synergistic increases in gross chromosomal rearrangement (GCR) rates, accumulation of a broad spectrum of GCRs, and hypersensitivity to replication stress. The double mutants have severe replication defects and accumulate aberrant replication intermediates. None of the individual mutations cause large increases in GCR rates; however, defects in MRC1, CSM3 or TOF1 cause activation of the DNA damage checkpoint and replication defects. We propose a model in which Htz1 deposition and retention in chromatin prevents transiently stalled replication forks that occur in mrc1, tof1, or csm3 mutants from being converted to DNA double-strand breaks that trigger genome instability.

Highlights

In our previous study of systematically generated mutant strains, we observed that combining mutations affecting Swr1 chromatin-remodeling complex (SWR-C) or its substrate, Htz1, and the replication fork progression proteins Mrc1, Tof1 or Csm3 resulted in synergistic increases in dGCR rate, as assessed by semi-qualitative patch scores6
The mrc1Δ swr1Δ and mrc1Δ htz1Δ double mutants and the mrc1Δ swr1Δ htz1Δ triple mutant had similar increases in dGCR rates (Supplementary Table 1; Supplementary Data 1), which is consistent with the hypothesis that Htz1 and SWR-C act in the same pathway, i.e., Htz1 deposition, to prevent the accumulation of gross chromosomal rearrangement (GCR) in the absence of Mrc1
Combining mrc1Δ or mrc1-1-843 with either tof1Δ or csm3Δ caused increased GCR rates, and combining mrc1Δ or mrc1-1-843 with the tof1Δ swr1Δ or csm3Δ swr1Δ double mutations caused even greater increases in GCR rates (Supplementary Table 1; Supplementary Data 1). These results suggest that mutations affecting Mrc1 and the Tof1Csm3 complex impair redundant replication functions, leading to increased GCR rates, which are further exacerbated in the absence of SWR-C/Htz1

Summary

Introduction

We identify a role for the histone Htz, which is deposited by the Swr chromatin-remodeling complex (SWR-C), in preventing genome instability in the absence of the replication fork/replication checkpoint proteins Mrc, Csm, or Tof. The htz1Δ and/or swr1Δ mutations cause sensitivity to DNA-damaging agents, decreased sisterchromatid cohesion, defects in recruitment of DNA doublestrand breaks (DSBs) to the nuclear periphery, modest defects in resection of DSBs, a small decrease in non-homologous end joining, a small (~twofold) increase in the rate of point mutations when combined with the pol3-L612M mutation in DNA polymerase δ that increases base misincorporation rates, and synergistic growth interactions with mutations affecting chromosome segregation. Defects in MRC1, CSM3, and TOF1 cause defects in cohesion establishment, but these defects appear to define parallel pathways, one involving MRC1 and the other involving TOF1 and CSM343

Methods

Results

Conclusion